MolNFT v1 · #18250 · protein
Crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme a decarboxylase
1PIX · Glutaconyl-CoA decarboxylase a subunit: “Crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme a…”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.83). MolNFT v1 #18250…
- PDB
- 1PIX
- Type
- protein
- Length
- 1,172 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaconyl-CoA decarboxylase a subunit
- EC
- 4.1.1.70
- UniProt
- Q06700
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutaconyl-CoA decarboxylase a subunit (EC 4.1.1.70) | protein | 586 | 40% helix, 17% strand | Q06700 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.83 | 0.84 | 116 | FMT, SO4 |
| 2 | 1196 | 0.76 | 0.78 | 108 | empty |
| 3 | 971 | 0.75 | 0.77 | 86 | empty |
| 4 | 143 | 0.51 | 0.80 | 35 | empty |
| 5 | 76 | 0.35 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 5123 Ų buried · 63 hydrogen bonds · protein-protein
Compared structures
- 1PIX · Crystal structure of the carboxyltransferase subunit of the bacterial ion pump… · the same entry in another collection · chain A against A, TM-score 1.00
- Q06700 · AlphaFold monomer V2.0 prediction for glutaconyl-CoA decarboxylase subunit alpha (Q06700) · a predicted model of the same protein · chain B against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q06700
- Elsewhere: RCSB PDB 1PIX · PDBe 1PIX · UniProt Q06700
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